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0.20Parasite Experiment OntologyParasite Experiment ontology version 0.10Parasite Research, Biomedicine, Provenance, Experiment DataS.S. Sahoo, D.B. Weatherly, R. Mutharaju, P. Anantharam, A. Sheth, R.L. Tarleton, “Ontology-driven Provenance Management in eScience: an Application in Parasite Research”, The 8th International Conference on Ontologies, DataBases, and Applications of Semantics, (ODBASE 2009), Vilamoura, Algarve-Portugal, pp.992-1009, Nov 02 - 04, 2009Satya S. Sahoo, Brent Weatherly, Priti Parikh, Flora LoganThe Parasite Experiment ontology was developed as part of the NIH-funded "Semantics and Services enabled Problem Solving Environment for Tcruzi" project (Grant#1R01HL087795-01A1).
The Kno.e.sis center, Computer Science and Engineering Department, Wright State University, USA and the Tarleton Lab, Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, USA collaborated to create this ontology.
Resource page: http://knoesis.wright.edu/trykipediaThis property links a process to all its input value. The input values belong to only data_collection (parameter values are linked to process by property has_parameter).This property links a process to all its output value. The output values belong to only data_collection (parameter values are linked to process by property has_parameter).If two paralogous genes occur in the same gene, they are allelesGrowth of specific lifecycle stage of Trypanosoma cruzi.Trypanosoma cruzi cells in growth mediumAn unique identifier given to a DNA or protein sequence record.For diploid (or polyploid) organisms where a knockout construct plasmid is created for each allele of a gene, the allele_designation is the assignment of allele number for a particular knockout plasmid.Selection to produce a population of genetically-identical individualsA sample of cells that has been grown from a single starter cell.A cloned_sample_designate is the instance of cloned_sample that is chosen by a researcher to be the clone of a particular strain that should be used for subsequent experiments involving that strain.Liquid broth designed to support the growth of microorganisms. Contains a mixture of essential nutrients, as well as nutrients designed to optimise growth.An aspect of the culture that defines certain characteristics of an experiment.Any chemical substance that, when absorbed into a cell, alters normal cell functionAttributes of the specified drug.Concentration of drug used in experiment.A plasmid that is used to introduce and express a specific drug resistant gene into a target cellA sample that has been grown under selective drug pressure, that is, in the presence of a normally lethal compound.The presence of a drug used to put selective pressure on cells which are expressing a protein conferring resistance against that drug.The justification for performing a particular experiment.Any notes made by a researcher for the design, tracking, and results of experimentsA freezer is a dry, cold-storage machine.Where freezer is located.The method by which a gene knock out is producedA labelled cDNA probe is incubated with the microarray.Position of the kinetoplast in relation to the nucleus.A plasmid that is used to introduce and express a specific drug resistant gene into a target cell, whilst disrupting or deleting a native geneA plasmid that is used to introduce and express a specific drug resistant gene into a target cell, whilst disrupting or deleting a native geneThe process of taking one or more plasmids containing drug resistance and target region sequences and creating a knockout plasmid.The top-level protocol by which a target gene is knocked-out from an organism.The method by which a specific allele of a gene is knocked-out.A cDNA probe is labelled with a radioactive marker.Any parameters used by researchers to describe or track the progress of experiments that are specific to a particular lab's protocols.The log, base 2, of the signal intensity in channel 1 vs channel 2 for a microarray probe in a two-color hybridization.Cluster of significant genes that were identified using ANOVA.A machine that scans a microarray, reading the fluorescent signal intensityA macromolecule composed of chains of monomeric nucleotidesThis is a computational process to assign a given oligonucleotide to set of target genesThe sum of the spectral counts for peptides hitting a particular gene or protein group.Any observable characteristic or trait of an organismThe process by which a plasmid is madeCurrent step in the plasmid cloning process.A technique for amplifying DNA sequences in vitro by separating the DNA into two strands and incubating it with oligonucleotide primers and DNA polymerase.Incubation of microarray used to block nonspecific binding sites.Assuming many genes that could be targeted for knockout, the priority is used to order when the particular genes are targeted.Arbitrary number assigned to a protein group.22Analysis of proteome; i.e., all the proteins expressed by an organism.The purity of the organism of interest in a complex sample which may contain media, contaminants, and other componentsA researcher is any individual involved in the experimental processes.Notes from researchers designing the experiment (renamed Other Notes)An entity that is representative of a class, also known as a specimen.The method by which a sample is characterized molecularly and phenotypically.As done by microarray plate reader, reading the signal intensities of the microarray.The percent coverage for the protein based upon the matched peptide sequences (can be calculated) (source: Mass spectrometry Ontology).Copying a nucleotide or amino acid sequence from a database.Raw fluorescence intensity for spots on microarray following hybridisation.The total number of time a given spectrum is detected in an MSMS run.Process to determine purity of T. cruzi lifecycle sample.It is a standard deviation for biological replicates in microarray experiments.Different concepts or measures used in statistical analysis.Status is an administrative parameter used to track the progress of experiments.The process by which a new strain of an organism is created via gene knockout.The protocol containing all sub-processes for strain creation.A plasmid that contains some portion of the sequence of a gene targeted for genetic manipulation.Notes from the researchers performing the experiment in the lab (renamed KO Log)Temperature at which experiment is carried out. Usually measured on the Celsius scale.The method by which a transcriptome experiment is carried outThe genome of an organism after transfection of a plasmid into its genome.T. cruzi sample that has been transfected with a plasmidThe act of introducing a DNA molecule into an organism by electroporation.Buffer (or media) used during the transfection process.Machine used to transfect cells with plasmid DNA, often by electroporation.A term that expresses the function of a gene product (source: NCI Thesaurus).Analysis using microarray technology (e.g., cDNA arrays to see gene expression or protein microarrays to profile the pattern of proteins). (source: NCI Thesaurus)A statistical way of expressing knowledge or belief that an event will occur or has occurred.PLO:000015the nonflagellate intracellular morphologic stage in the development of Leishmania species parasitesPLO:000017the epimastigote stage of Trypanosoma brucei, found in the tsetse flyPLO:000041Infectious stage of Trypanosoma brucei, found in tsetse fly salivary glands.PLO:000024trypomastigote morphological form of Trypanosoma bruceiPLO:000016the nonflagellate intracellular morphologic stage in the development of Trypanosoma cruzi parasitesPLO:000018the epimastigote stage of Trypanosoma cruzii, found in the insect vectorPLO:000042Infectious stage of Trypanosoma cruzi, found in reduviid bug hindgut.PLO:000025trypomastigote morphological form of Trypanosoma cruziPLO:000005The nonflagellate intracellular morphologic stage in the development of trypanosomatid parasitesPLO:000026A trypomastigote found in the mammalian host blood stream.PLO:000006A developmental stage in trypanosomes. The undulating membrane is shortened and the flagellar pocket and the kinetoplast are anterior to the nucleus; in the previous stage they are near the tail and behind the nucleus. This stage occurs in the insect host.PLO:000011An organism that hosts a parasitePLO:000001Period of time in the lifecycle of a cellPLO:000019Infectious promastigote stage of Leishmania speciesPLO:000027infectious stage of Trypanosoma speciesPLO:000002Any living structure capable of growth and reproduction.PLO:000003a variant of an organism, or an inbred organism used for experimental purposesPLO:000020non-infective promastigote stage of Leishmania species, found in the insect vectorPLO:000028dividing form of Trypanosoma brucei found in the tsetse fly midgutPLO:000007One of the morphological stages in the development of Leishmania species, characterized by a free anterior flagellum and the kinetoplast at the anterior end of the body.PLO:000008The characteristic developmental stage of trypanosomes, a leaf-like form, with undulating membrane and flagellum.Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication (source: Sequence Ontology).The DNA sequences extending on either side of a specific locus (source: Sequence Ontology).A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. (source: Sequence Ontology)A genome is the sum of genetic material within a cell or virion (source: Sequence Ontology).The region between two known genes (source: Sequence Ontology).Small DNA fragments (probes) chemically synthesized at specific locations (spots) on a microarray chip. Probes are typically 25-60 nucleotide long.an extra-chromosomal DNA molecule separate from the chromosomal DNA which is capable of replicating independently of the chromosomal DNA - normally circular and double stranded. Often referred to as a vector in molecular biology.A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids (source: Sequence Ontology).Concept (imported from OWL Time ontology) to describe temporal entities.